12086 results for "cancer rna-seq"

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• Comprehensive molecular profiling of ETMR

  ETMR RIPSeq

  Dataset EGAD00001004802

• whole exome seq

  whole exome sequencing data

  Dataset EGAD00001004464

• Exome

  Exome Seq for EGAS00001001845

  Dataset EGAD00001002160

• MRC 60 snRNA-seq

  This dataset includes snRNA-seq generated from post-mortem brain and genotype from 60 individuals. The snRNA-seq data was generated using the 10X Single Cell Next GEM Chip targeting a minimum 5,000 nuclei per sample and libraries prepared using the Chromium Single Cell 3′ Library and Gel Bead v3 kit according to manufacturer’s instructions. cDNA libraries were sequenced using the Illumina NovaSeq 6000 system at a minimum sequencing depth of 30,000 paired-end reads per nucleus. Samples were pooled (max 4 per pool) and sequenced over 4 lanes. Pool-specific genotype files (containing genotype information at individual level) were used to demultiplex mapped pools into individual-level single-cell data. Donor DNA from samples processed at Imperial College were genotyped using the Illumina Infinium Global Screening Array v2.0.

  Dataset EGAD50000000965

• scRNA-seq of total bone marrow mononuclear cells and CD3+ T cells of multiple myeloma patients and healthy donors

  The study includes 50 scRNA-seq samples of bone marrow aspirates of 11 multiple myeloma patients and 3 healthy donors generated with the 10x Genomics platform (Chromium Single Cell 3’ Solution v2). For the multiple myeloma patients, paired longitudinal samples are available from initial diagnosis and long-term surivor state. For each patient and timepoint, total bone marrow mononuclear cells and CD3+ T cells have been sequenced separately.

  Study EGAS00001006980

• Whole Exome and RNA Sequencing of 22 Patient-Derived Xenografts from Estrogen Receptor-Positive Breast Cancers

  We performed RNA and whole exome sequencing on 22 patient-derived xenografts (PDX) from estrogen receptor-positive (ER+) breast cancers, in the presence and absence of estradiol (E2) supplementation. Exome coverage across more than 3,500 clinically relevant genes that previously were covered below 20X (~2.72Mb) was achieved. On average, 11.2Gb of unique sequence data were generated with 95.3% of the bases in the exome design covered to 20x read depth or greater. RNA sequencing was generated from xenograft tumors. Between 50 and 85M total reads were performed. The average strand-specificity and rRNA rate was 98% and 1.5%, respectively. Transcripts for 17,000 to 27,087 genes were detected in these samples.

  Study phs003324

• RNA sequecing of primary B cells infected with Epstein-Barr virus (EBV) or stimulated with heat-inactivated EBV

  Naïve (CD27-IgD+) B cells were isolated from buffy coat preparations of healthy donors using CD19 magnetic beads, followed by reals of CD19 beads and incubation with IgD-biotin and anti-biotin magnetic beads. B cells were infected with EBV by spinoculation or stimulated with heat-inactivated EBV and control cells were left uninfected. RNA was extracted immediately after isolation in un-infected B cells. From EBV-infected B cells and B cells stimulated with heat-inactivated virus, RNA was extracted 24 and 96 hours after infection / stimulation.

  Dataset EGAD50000000305

• Ribosomal profiling on Epstein-Barr virus transformed B-lymphoblastoid cell lines

  Epstein-Barr virus-transformed B-lymphoblastoid cell lines from six individuals (HG00114, HG00282, NA12005, NA12044, NA12717 and NA12751) of the GEUVADIS Project were selected for ribosomal profiling. For each EBV-LCL, 20 million cells were treated with 2 μg/ml harringtonine and 100 μg/ml cycloheximide. After lysing cells in lysis buffer supplemented with 100 μg/ml cycloheximide, ribosome complexes were purified by density purification. Small RNA molecules were isolated using the NucleoSpin miRNA Kit (Bioke, Leiden, Netherlands), followed by RNA PAGE gel separation. Universal linkers were added after dephosphorylation. After reverse transcription, the cDNA was circularized and, after ribosomal RNA depletion, barcoded and sequenced on Illumina NextSeq 500.

  Dac EGAC50000000209

• Spinocerebellar ataxia type 3 RNA-sequencing study

  RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

  Study EGAS00001004241

• DIPG RNA and exome sequencing

  DIPG is a paediatric high-grade glioma that diffusely infiltrates the brainstem and is the leading cause of paediatric brain tumour death. Here we performed RNA and whole exome sequencing on DIPG and control samples to analyse transcriptomic and genetic alterations associated with this devastating disease, and to understand the relationship between them.

  Study EGAS00001004749